I will try to answer your questions to the best of my knowledge but don't bash me if some wrong information slips through. I have already taken a test drive and am going to pick up my 400h this weekend (fingers crossed).
iPod Aux In: I didn't see one in the stereo console but if you buy a rear entertainment system (lexus installed not aftermarket), it comes with a "red, white, yellow" (composite) input jack with 110v AC inlet both in the cargo hold behind the rear passenger seats on the right. Not sure if you can adapt an ipod to feed the audio through there and besides who would want to put the ipod so far away from the driver seat. I have an ipod too and betting on getting a cassette tape adapter for it.
GPS can be seen on the rear lcd screen and even dvd movie can be seen in the front screen as long as the car is parked. You can even input the navigation destination using the remote for the rear entertainment system. Some have warned that the flip down lcd screen hinders the center rear view vision and also is not as convenient as 2 seperate screens behind the headrests.
I don't think it can play mp3s. not sure about cd-r's or dvd-rws. Once I get my 400h with rear seat entertainment, you will hear from the horse's mouth

Wait for my response early next week!